MolNFT v1 · #188391 · protein

Single-particle cryo-EM structure of the waal O-antigen ligase in its ligand bound state

7TPG · Putative cell surface polysaccharide POLYMERASE/LIGASE: “Single-particle cryo-EM structure of the waal O-antigen ligase in its ligand bound state”. Electron microscopy, 1 ligand (GPP), 7 pockets (best druggability 0.83). MolNFT v1…

PDB: 7TPG
Type: protein
Length: 626 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative cell surface polysaccharide POLYMERASE/LIGASE; Fab heavy (H) chain; Fab light…
UniProt: Q1LJU1
Ligands: GPP
Pockets: 7 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Putative cell surface polysaccharide POLYMERASE/LIGASE	protein	403	74% helix, 0% strand	Q1LJU1
H	Fab heavy (H) chain	protein	119	3% helix, 49% strand	—
L	Fab light (L) chain	protein	104	0% helix, 40% strand	—

Ligands and binding sites

GPP · Geranyl diphosphate · ligand · chains B, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.83	0.84	118	GPP
2	172	0.44	0.74	27	empty
3	89	0.42	0.78	14	empty
4	50	0.35	0.80	18	empty
5	52	0.34	0.78	14	empty

Interfaces

3 interfaces between chains.

H–L · 948 Å² buried · 9 hydrogen bonds · protein-protein
B–H · 820 Å² buried · 4 hydrogen bonds · protein-protein
B–L · 478 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7TPG · Single-Particle Cryo-EM Structure of the WaaL O-antigen ligase in its ligand bound state · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q1LJU1
Elsewhere: RCSB PDB 7TPG · PDBe 7TPG · UniProt Q1LJU1

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